Sequence
atgc intronic sequence ATGC exonic sequencegtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60920.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60920.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 3'ss of exon 19
gtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
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-------------gtacatgaacacaa-catataatttttctatgctgttgttggtagctt-------tgaatctcagt--atattcaa-----tttcttcagATTAGCAATTTTGAGTACTTGATGGAACTGAACACACTGGCTGGACGAAGTTACAATGACATAACTCAG
upper sequence: AT3G60920.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G044143_T01 (Zea mays), 3'ss of exon 19
gtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
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-------------------------------gtacacatacattgtcct-----gtgctatatgttggtagttttaatacctaaccatgtctaatttgttcagATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAG
upper sequence: AT3G60920.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 20
gtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
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gtaag-agaaactgtctcatgtatcaaatctgtgatattatatt----ttctaaagctcctctctctctcacacaagccacaa---ttatgaccattctgcagATTAGCAACTTTGAATATCTAATGCAACTCAATACACTGGCTGGACGTAGTTATAATGACATAACTCAG
upper sequence: AT3G60920.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: PP1S62_38V6.1 (Physcomitrella patens), 3'ss of exon 20
gtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatc---ttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
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-cagtagtattgttttgccaatcag-agcggacctttctaacttaattttttcgtaaaaattcggc-gcaacgct---ttaatctttggggttggattttgaacagATCAGTAATTTCGAGTACTTAATGCAGCTGAACACTTTGGCTGGCAGATCATACAATGATATTACTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
cagtaac putative branch site (score: 2)
ctttgcatcttttct putative PPT
aataacat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccagagaatatcctttatctccatcatgcaatttcattttgttcccttgaataacatctggcagtaactctcgctggatactttgcatcttttctgcagATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA